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FAQ and support

FAQ

How do I access the IWGSC reference sequence?

The IWGSC reference sequence is available to download, BLAST and browse here .

 

How do I launch a BLAST?

Look at the dedicated BLAST page .

 

How do I cite this resource?

Please quote the Alaux et al. Genome Biology 2018 paper.

 

What data are public and what data need a specific access?

Look at the Access status page .

 

How do I browse the IWGSC reference sequence?

Use the dedicated browser .

 

What are the IWGSC RefSeq IDs of gene models nomenclature ?
 

v1.0: TraesCS1A01GXXXXXX.1

v1.1: TraesCS1A02GXXXXXX.1

Traes: Triticum aestivum (species name)

CS: Chinese Spring (variety name)

1A: chromosome name

0[12]: version of annotation 01=v1.0 / 02=v1.1

G: genomic sequence

XXXXXX: 6 digit number

.1: splicing variant #1

While updating the IWGSC RefSeq Annotation from v1.0 to v1.1, the "6 digit number" was NOT modified. For instance, TraesCS1A01G000100.1 and TraesCS1A01G000100.1 define the two IDs of the same gene model in versions v1.0 and v1.1, respectively.

 

What is the survey sequence contig nomenclature?

example:

>IWGSC_chr3B_ab_k71_contigs_longerthan_200:10567088 3505 62189 4936946+,...,988109+

The nomenclature of the contigs is the standard output from the ABySS assembler.

The contig id comes first (10567088), then the contig length (3505), then the absolute k-mer coverage (62189). These three columns will exist for all contigs. In addition, paired-end contigs (scaffolds) have a fourth column which shows the list of contigs that comprise the scaffold. In the example, contig 10567088 is comprised of contig 4936946 and contig 988109, both in the same direction (+)

 

Another question? please contact urgi-support[at]inra.fr

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Update: 12 Aug 2019
Creation date: 04 Dec 2014